gearslaboratory/gears-singularity:gears-lidr
$ singularity pull shub://gearslaboratory/gears-singularity:gears-lidr
Singularity Recipe
BootStrap: debootstrap
OSVersion: xenial
MirrorURL: http://archive.ubuntu.com/ubuntu/
Include: bash
##### GEARS Lab General-use Singularity image. Contains R, GDAL, GRASS, and other code...
%post
locale-gen en_US.UTF-8
sed -i 's/main/main restricted universe/g' /etc/apt/sources.list
echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | apt-key add -
apt-get update
# Latest R
apt-get install -y software-properties-common python-software-properties
# add-apt-repository ppa:edd/r-3.5
apt-get update
# Install R, openmpi, misc. utilities:
apt-get install -y libopenblas-dev r-base-core r-base-dev libcurl4-openssl-dev libopenmpi-dev openmpi-bin openmpi-common openmpi-doc openssh-client openssh-server libssh-dev wget vim git nano git cmake gfortran g++ curl wget python autoconf bzip2 libtool libtool-bin libxml2-dev
# GRASS GIS and QGIS:
apt-get install -y software-properties-common python-software-properties
add-apt-repository ppa:ubuntugis/ppa
apt-get update
apt-get install -y grass libgdal-dev libproj-dev python-gdal python3-gdal qgis python-qgis
# Miscellaneous other installs.
# libudunits2-dev is needed for the package "sf"
apt-get install -y libudunits2-dev
# SVN:
apt-get install -y subversion
# Clean up the installations...
apt-get clean
# Install required R packages
R --slave -e 'install.packages(c("doMPI","XML","raster","rgdal","rgeos","RStoolbox","devtools","sf","foreach","R.utils","spatial.tools","gdalUtils","randomForestSRC","remotes","future"), repos="https://cloud.r-project.org/")'
# Install lidR:
add-apt-repository ppa:glasen/freetype2
apt-get update && apt-get install -y freetype2-demos
# apt-get install -y freetype
R --slave -e 'install.packages(c("lidR"), repos="https://cloud.r-project.org/")'
# Install latest GDALUtils:
# R --slave -e 'remotes:::install_svn("svn://r-forge.r-project.org/svnroot/gdalutils/pkg/gdalUtils")'
# Install latest spatial.tools:
# R --slave -e 'remotes:::install_svn("svn://r-forge.r-project.org/svnroot/spatial-tools/pkg/spatial.tools")'
# ESPA tools:
R --slave -e 'remotes:::install_svn("svn://r-forge.r-project.org/svnroot/espa-tools/pkg/espa.tools")'
# Install beta of mmap for now:
R --slave -e 'devtools:::install_git("https://github.com/gearslaboratory/gears-singularity.git",subdir="singularity_additional_data/general_use/mmap")'
# Install pronghorn-tweaked rslurm:
# R --slave -e 'devtools:::install_github("jgrn307/rslurm")'
# wine:
mkdir -p /APPS /PROFILES
chmod 0777 /APPS /PROFILES
dpkg --add-architecture i386
apt-get update && apt-get -y install wget less vim software-properties-common python3-software-properties apt-transport-https winbind
wget https://dl.winehq.org/wine-builds/Release.key
apt-key add Release.key
apt-add-repository https://dl.winehq.org/wine-builds/ubuntu/
apt-get update && apt-get install -y winehq-stable winetricks # this installs Wine2
apt-get clean
# lastools
cd ‾
wget http://lastools.org/download/LAStools.zip
unzip LAStools.zip
mv LAStools /opt/
# TODO: shortcuts/licensing
### SLURM FROM WITHIN THE CONTAINER VIA SSH
echo '#!/bin/bash
ssh $USER@$HOSTNAME sacct $1' >> /usr/local/bin/sacct
echo '#!/bin/bash
ssh $USER@$HOSTNAME sacctmgr $1' >> /usr/local/bin/sacctmgr
echo '#!/bin/bash
ssh $USER@$HOSTNAME salloc $1' >> /usr/local/bin/salloc
echo '#!/bin/bash
ssh $USER@$HOSTNAME sattach $1' >> /usr/local/bin/sattach
echo '#!/bin/bash
ssh $USER@$HOSTNAME sbatch $1' >> /usr/local/bin/sbatch
echo '#!/bin/bash
ssh $USER@$HOSTNAME sbcast $1' >> /usr/local/bin/sbcast
echo '#!/bin/bash
ssh $USER@$HOSTNAME scancel $1' >> /usr/local/bin/scancel
echo '#!/bin/bash
ssh $USER@$HOSTNAME scontrol $1' >> /usr/local/bin/scontrol
echo '#!/bin/bash
ssh $USER@$HOSTNAME sdiag $1' >> /usr/local/bin/sdiag
echo '#!/bin/bash
ssh $USER@$HOSTNAME sgather $1' >> /usr/local/bin/sgather
echo '#!/bin/bash
ssh $USER@$HOSTNAME sinfo $1' >> /usr/local/bin/sinfo
echo '#!/bin/bash
ssh $USER@$HOSTNAME smap $1' >> /usr/local/bin/smap
echo '#!/bin/bash
ssh $USER@$HOSTNAME sprio $1' >> /usr/local/bin/sprio
echo '#!/bin/bash
ssh $USER@$HOSTNAME squeue $1' >> /usr/local/bin/squeue
echo '#!/bin/bash
ssh $USER@$HOSTNAME sreport $1' >> /usr/local/bin/sreport
echo '#!/bin/bash
ssh $USER@$HOSTNAME srun $1' >> /usr/local/bin/srun
echo '#!/bin/bash
ssh $USER@$HOSTNAME sshare $1' >> /usr/local/bin/sshare
echo '#!/bin/bash
ssh $USER@$HOSTNAME sstat $1' >> /usr/local/bin/sstat
echo '#!/bin/bash
ssh $USER@$HOSTNAME strigger $1' >> /usr/local/bin/strigger
echo '#!/bin/bash
ssh $USER@$HOSTNAME sview $1' >> /usr/local/bin/sview
cd /usr/local/bin
chmod 755 sacct salloc sbatch scancel sdiag sinfo sprio sreport sshare strigger sacctmgr sattach sbcast scontrol sgather smap squeue srun sstat sview
cd ‾
Collection
- Name: gearslaboratory/gears-singularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/gearslaboratory-gears-singularity-gears-lidr |
collection name | gearslaboratory/gears-singularity |
branch | master |
tag | gears-lidr |
commit | 402c63481bc49a8a88ed42ed482a36ac3773c36d |
version (container hash) | f736dbe780a767209ebd6435830eb1c3 |
build date | 2019-02-19T17:41:52.639Z |
size (MB) | 3650 |
size (bytes) | 1191559199 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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